ABSTRACT The Molecular Cytogenetics Core provides valuable scientific and technical support to MSK investigators exploring the role of chromosomal instability in cancer. This is accomplished through appropriate and efficient experiment design, custom multi-color DNA-FISH probe design and development, data analysis and interpretation, and support with manuscript/grant preparation. Currently, the Core provides 2 main categories of specialized service that operate at the single-cell level on a variety of human and animal model research samples: conventional karyotyping and fluorescence in situ hybridization (FISH). Conventional karyotyping is routinely performed to confirm cell line identity, screen targeted mouse ESC clones intended for blastocyst injection, monitor the stability of cultured stem cells over time, and measure chromosomal instability/heterogeneity as an experimental endpoint. Over the years, the Core has assembled a broad range of molecular cytogenetics resources (plasmids, BAC clones, individual whole chromosome painting probes), allowing the Core to provide FISH services at significantly lower cost. FISH-based assays are routinely employed to map genes or transgene integration sites, detect aneuploidy/chromosomal instability, co-detect DNA/protein and assess intra-tumoral heterogeneity; tests include custom probe development, locus-specific FISH, whole-chromosome painting (WCP), spectral karyotyping (SKY), Q-FISH, and Immuno-FISH. The Core is equipped with 5 modern Fluorescence imaging systems including 2 with a wide range of applications that can be fully or partially automated. The Core also provides training in tissue culture, karyotyping, and FISH. During the past grant period, the services and collaborative work provided by the Molecular Cytogenetics Core have supported the research of 84 investigators from 8 research program.